乳腺癌lncRNAs表达谱的检测

目的 初步探讨人乳腺癌lncRNAs基因表达谱的筛选。方法 在EBI数据库中的Array Express子数据库选取两组代表乳腺癌基因表达的基因芯片数据,从一组数据下载原始CEL数据文件,运用RMA(RobustMultichip Average)方法对原始CEL文件进行标准化及背景校正。得到乳腺癌与癌旁组织中的探针表达谱矩阵,将其与NetAffx 注释文件结合。提取出RefSeq转录本 ID和(或)Ensembl基因ID的探针集。对于Refseq ID的探针集,只保留那些NR者(代表非编码RNA)。对于Ensembl 基因 ID的探针集,只保留注释为LncRNA,加工过的 转录本或“misc_RNA”。对上述步骤得到的数据进行过滤,得到存在差异表达的lncRNA数量,将这一结果在另一组乳腺癌芯片数据中进行验证。结果 共筛选出表达差异显著且方向一致的18个LncRNA,其中2种LncRNAs表达明显上调,16种LncRNAs表达明显下调。 结论 筛选出与乳腺癌相关的差异表达lncRNAs,为进一步研究其在乳腺癌中的作用奠定基础。

A preliminary Study of LncRNA Expression Profile in Breast Cancer

Objective To investigate the expression patterns of long non-coding RNAs (lncRNAs) in breast cancer. Methods Two publicly available human exon arrays for breast cancer and data for the corresponding normal tissue were downloaded from the ArrayExpress Microarray Database at EBI. We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P-values below 0.01 were considered differentially expressed. An independent data set was used to validate the results. Resultswe identified 18 lncRNAs that were differentially expressed in breast cancer: two LncRNAs genes were up-regulated and 16 LncRNAs genes were down-regulated. Conclusion We identified a set of lncRNAs differentially expressed in breast cancer, providing useful information for discovery of new biomarkers and therapeutic targets in breast cancer.